CDAT Migration Phase 2: Add CDAT regression test notebook template an…

…d fix GH Actions build (#743)

- Add Makefile for quick access to multiple Python-based commands such as linting, testing, cleaning up cache and build files
- Fix some lingering unit tests failure
- Update `xcdat=0.6.0rc1` to `xcdat >=0.6.0` in `ci.yml`, `dev.yml` and `dev-nompi.yml`
- Add `xskillscore` to `ci.yml`
- Fix `pre-commit` issues

.pre-commit-config.yaml

@@ -26,13 +26,13 @@ repos:
     rev: 6.1.0
     hooks:
       - id: flake8
-        args: ["--config=setup.cfg"]
+        args: [--config=setup.cfg]
         additional_dependencies: [flake8-isort==6.1.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.5.1
     hooks:
       - id: mypy
-        args: ["--config=pyproject.toml"]
+        args: [--config=pyproject.toml]
         additional_dependencies:
           [dask, numpy>=1.23.0, xarray>=2023.3.0, types-PyYAML]

Makefile

@@ -0,0 +1,82 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+# To run these commands: make <COMMAND>
+# ==================================================
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+# Clean local repository
+# ----------------------
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr conda-build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr tests_coverage_reports/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -f coverage.xml
+	rm -fr .pytest_cache
+	rm -rf .mypy_cache
+
+# Quality Assurance
+# ----------------------
+pre-commit:  # run pre-commit quality assurance checks
+	pre-commit run --all-files
+
+lint: ## check style with flake8
+	flake8 e3sm_diags tests
+
+test: ## run tests quickly with the default Python and produces code coverage report
+	pytest
+	$(BROWSER) tests_coverage_reports/htmlcov/index.html
+
+# Documentation
+# ----------------------
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -rf docs/generated
+	cd docs && make html
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+# Build
+# ----------------------
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install